Updated PhyloToL Part 1: GF assignment (markdown)

PhyloToL-Part-1:-GF-assignment.md

@@ -130,5 +130,21 @@ The parameter options are:
 | --genetic_code| str| Path to a file, Universal | If all of your taxa use the same genetic code, you may enter it here|
 | --databases| str| Path to databases folder | The folder should contain all 3 databases|
 
+## Output
+
+When you run PhyloToL part 1 on **transcriptomic data** it will generate a folder called "Output" in the same folder as your "Scripts" folder. This Output folder will have the following structure:
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+<img src="https://github.com/Katzlab/PhyloToL-6/blob/main/Other/PTL_trans_output_1.png" width="30%">
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+The "ReadyToGo" folder contains the final cleaned output of PhyloToL part 1. The ReadyToGo_AA folder contains translated sequences, and these are the files (one per input sample) that should be input to PhyloToL part 2. The ReadyToGo_NTD folder contains the same sequences, untranslated, and ReadyToGo_TSV contains the a summary of the best Diamond hit in the Hook (or other GF reference) database for each sequence, which determines OG assignment. The PerSequenceStatSummaries and PerTaxonSummary files are also final products, giving basic sequence descriptions for all taxa in spreadsheet form.
+
+PhyloToL part 1 also provides all intermediate files used in producing the above finalized outputs. Of greatest interest to most users here are likely to be the files in the `Intermediate/TranslatedTranscriptomes` folder, in which all intermediate files for each taxon are stored. Most importantly, users can find a record of all Diamond hits against the Hook Database (not filtered to keep only the best hits) in the file `DiamondOG/allOGresults.tsv`. This could be useful in trying to assess alternative gene family assignments. See the headers of each PhyloToL part 1 scripts for a description of the individual intermediate outputs.
+
+The output of PhylToL part 1 when run on **genomic data** is very similar.
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